If designing a custom capture array for a subset of genes to sequence in an NGS/SNP study, does it make sense to include the coordinates of known-associated regulatory regions as well as the (non-overlapping) exonic coordinates for all known transcripts produced by the gene?
I would guess that I should be able to easily extract information like this from Ensembl/UCSC.
I assume that including associated regulatory regions may increase the possibility of finding meaningful variants?
Opinions welcome. I am new to all of this.